The analyses of HIV-1 quasispecies in HIV-infected subjects by the application of single genome amplification assay / 中华预防医学杂志

ABSTRACT

<p><b>OBJECTIVE</b>To establish the single genome amplification (SGA) method and analyze the quasispecies in HIV-infected patients.</p><p><b>METHODS</b>All 6 sample RNA acquired in 2010 in Shenzhen and genetic sequenced as overlap peaks were extracted and diluted to a single copy, nest-PCR after one step RT-PCR was employed to amplify HIV-1 genome, and then PCR products was purified and sequenced. Mega 4.02 software was used to analyze the genetic distance among HIV-1 quasispecies, and phylogenetic tree was constructed.</p><p><b>RESULTS</b>Our data showed that viral sequences derived from different patients were grouped into different clusters. Subcluster was also observed in several clusters, indicating these existed competition and preferential replication of certain viral strains. The genetic distance within one cluster of 6 samples were between 0.008 and 0.06, it was likely to associate with the duration since infection and viral load.</p><p><b>CONCLUSION</b>SGA is a useful approach to gain information on quasispecies, the genetic distance within one cluster may help to determine the infection time and immune escaping. The analysis of related affecting factors need more samples.</p>